LSD2_SCHPO
ID LSD2_SCHPO Reviewed; 1273 AA.
AC Q10135; Q9USA2;
DT 01-FEB-1996, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1996, sequence version 1.
DT 03-AUG-2022, entry version 139.
DE RecName: Full=Lysine-specific histone demethylase 2;
DE EC=1.-.-.-;
GN Name=lsd2; Synonyms=saf140, swm2; ORFNames=SPAC23E2.02;
OS Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Taphrinomycotina;
OC Schizosaccharomycetes; Schizosaccharomycetales; Schizosaccharomycetaceae;
OC Schizosaccharomyces.
OX NCBI_TaxID=284812;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=972 / ATCC 24843;
RX PubMed=11859360; DOI=10.1038/nature724;
RA Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A.,
RA Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S.,
RA Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M.,
RA Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S.,
RA Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S.,
RA Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D.,
RA Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P.,
RA Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K.,
RA O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M.,
RA Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N.,
RA Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A.,
RA Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R.,
RA Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M.,
RA Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A.,
RA Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A.,
RA Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H.,
RA Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S.,
RA Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C.,
RA Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A.,
RA Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M.,
RA del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S.,
RA Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R.,
RA Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G.,
RA Nurse P.;
RT "The genome sequence of Schizosaccharomyces pombe.";
RL Nature 415:871-880(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA] OF 201-404, AND SUBCELLULAR
RP LOCATION.
RC STRAIN=ATCC 38364 / 968;
RX PubMed=10759889; DOI=10.1046/j.1365-2443.2000.00317.x;
RA Ding D.-Q., Tomita Y., Yamamoto A., Chikashige Y., Haraguchi T.,
RA Hiraoka Y.;
RT "Large-scale screening of intracellular protein localization in living
RT fission yeast cells by the use of a GFP-fusion genomic DNA library.";
RL Genes Cells 5:169-190(2000).
RN [3]
RP FUNCTION, INTERACTION WITH LSD1, AND SUBCELLULAR LOCATION.
RX PubMed=16990277; DOI=10.1074/jbc.m606349200;
RA Nicolas E., Lee M.G., Hakimi M.-A., Cam H.P., Grewal S.I.S.,
RA Shiekhattar R.;
RT "Fission yeast homologs of human histone H3 lysine 4 demethylase regulate a
RT common set of genes with diverse functions.";
RL J. Biol. Chem. 281:35983-35988(2006).
RN [4]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=16823372; DOI=10.1038/nbt1222;
RA Matsuyama A., Arai R., Yashiroda Y., Shirai A., Kamata A., Sekido S.,
RA Kobayashi Y., Hashimoto A., Hamamoto M., Hiraoka Y., Horinouchi S.,
RA Yoshida M.;
RT "ORFeome cloning and global analysis of protein localization in the fission
RT yeast Schizosaccharomyces pombe.";
RL Nat. Biotechnol. 24:841-847(2006).
RN [5]
RP FUNCTION, IDENTIFICATION IN THE SWM HISTONE DEMETHYLASE COMPLEX, AND
RP INTERACTION WITH LSD1.
RX PubMed=17434129; DOI=10.1016/j.molcel.2007.02.023;
RA Lan F., Zaratiegui M., Villen J., Vaughn M.W., Verdel A., Huarte M.,
RA Shi Y., Gygi S.P., Moazed D., Martienssen R.A., Shi Y.;
RT "S. pombe LSD1 homologs regulate heterochromatin propagation and
RT euchromatic gene transcription.";
RL Mol. Cell 26:89-101(2007).
RN [6]
RP IDENTIFICATION IN THE SWM HISTONE DEMETHYLASE COMPLEX, AND FUNCTION OF THE
RP SWM COMPLEX.
RX PubMed=17440621; DOI=10.1371/journal.pone.0000386;
RA Opel M., Lando D., Bonilla C., Trewick S.C., Boukaba A., Walfridsson J.,
RA Cauwood J., Werler P.J., Carr A.M., Kouzarides T., Murzina N.V.,
RA Allshire R.C., Ekwall K., Laue E.D.;
RT "Genome-wide studies of histone demethylation catalysed by the fission
RT yeast homologues of mammalian LSD1.";
RL PLoS ONE 2:E386-E386(2007).
CC -!- FUNCTION: Catalytic component of the SWM histone demethylase complex
CC that specifically demethylates H3K9me2, a specific tag for epigenetic
CC transcriptional activation, thereby acting as a corepressor. Acts by
CC oxidizing the substrate by FAD to generate the corresponding imine that
CC is subsequently hydrolyzed. Has a role in regulating heterochromatin
CC propagation and euchromatic transcription. Also has a gene activating
CC role. {ECO:0000269|PubMed:16990277, ECO:0000269|PubMed:17434129,
CC ECO:0000269|PubMed:17440621}.
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692;
CC -!- SUBUNIT: Component of the SWM histone demethylase complex composed of
CC at least lsd1, lsd2, phf1 and phf2. Interacts directly with lsd1.
CC {ECO:0000269|PubMed:16990277, ECO:0000269|PubMed:17434129,
CC ECO:0000269|PubMed:17440621}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00267,
CC ECO:0000269|PubMed:10759889, ECO:0000269|PubMed:16823372,
CC ECO:0000269|PubMed:16990277}.
CC -!- SIMILARITY: Belongs to the flavin monoamine oxidase family.
CC {ECO:0000305}.
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DR EMBL; CU329670; CAA93114.1; -; Genomic_DNA.
DR EMBL; AB027920; BAA87224.1; -; Genomic_DNA.
DR PIR; T38292; T38292.
DR RefSeq; NP_592937.1; NM_001018338.2.
DR AlphaFoldDB; Q10135; -.
DR SMR; Q10135; -.
DR BioGRID; 278323; 6.
DR STRING; 4896.SPAC23E2.02.1; -.
DR iPTMnet; Q10135; -.
DR MaxQB; Q10135; -.
DR PaxDb; Q10135; -.
DR PRIDE; Q10135; -.
DR EnsemblFungi; SPAC23E2.02.1; SPAC23E2.02.1:pep; SPAC23E2.02.
DR GeneID; 2541832; -.
DR KEGG; spo:SPAC23E2.02; -.
DR PomBase; SPAC23E2.02; lsd2.
DR VEuPathDB; FungiDB:SPAC23E2.02; -.
DR eggNOG; KOG0029; Eukaryota.
DR HOGENOM; CLU_274764_0_0_1; -.
DR InParanoid; Q10135; -.
DR OMA; KMQWHVC; -.
DR PhylomeDB; Q10135; -.
DR BRENDA; 1.14.11.65; 5613.
DR PRO; PR:Q10135; -.
DR Proteomes; UP000002485; Chromosome I.
DR GO; GO:0000785; C:chromatin; IDA:PomBase.
DR GO; GO:0005829; C:cytosol; HDA:PomBase.
DR GO; GO:0033193; C:Lsd1/2 complex; IDA:PomBase.
DR GO; GO:0005634; C:nucleus; HDA:PomBase.
DR GO; GO:0003677; F:DNA binding; ISM:PomBase.
DR GO; GO:0140683; F:histone H3-di/monomethyl-lysine-9 demethylase activity; IDA:PomBase.
DR GO; GO:0016491; F:oxidoreductase activity; IBA:GO_Central.
DR GO; GO:0006338; P:chromatin remodeling; IMP:PomBase.
DR GO; GO:0033696; P:heterochromatin boundary formation; IPI:PomBase.
DR GO; GO:0016570; P:histone modification; IEA:UniProt.
DR Gene3D; 1.10.10.10; -; 1.
DR Gene3D; 1.10.30.10; -; 1.
DR Gene3D; 3.50.50.60; -; 2.
DR InterPro; IPR002937; Amino_oxidase.
DR InterPro; IPR036188; FAD/NAD-bd_sf.
DR InterPro; IPR009071; HMG_box_dom.
DR InterPro; IPR036910; HMG_box_dom_sf.
DR InterPro; IPR009057; Homeobox-like_sf.
DR InterPro; IPR007526; SWIRM.
DR InterPro; IPR036388; WH-like_DNA-bd_sf.
DR Pfam; PF01593; Amino_oxidase; 1.
DR Pfam; PF04433; SWIRM; 1.
DR SUPFAM; SSF46689; SSF46689; 1.
DR SUPFAM; SSF47095; SSF47095; 1.
DR SUPFAM; SSF51905; SSF51905; 1.
DR PROSITE; PS50118; HMG_BOX_2; 1.
DR PROSITE; PS50934; SWIRM; 1.
PE 1: Evidence at protein level;
KW Chromatin regulator; Coiled coil; DNA-binding; FAD; Flavoprotein; Nucleus;
KW Oxidoreductase; Reference proteome; Repressor; Transcription;
KW Transcription regulation.
FT CHAIN 1..1273
FT /note="Lysine-specific histone demethylase 2"
FT /id="PRO_0000116463"
FT DOMAIN 394..490
FT /note="SWIRM"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00247"
FT DNA_BIND 1115..1195
FT /note="HMG box"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00267"
FT REGION 199..237
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 542..1198
FT /note="Demethylase activity"
FT /evidence="ECO:0000250"
FT REGION 571..596
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1215..1273
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COILED 247..307
FT /evidence="ECO:0000255"
FT COILED 681..767
FT /evidence="ECO:0000255"
FT COMPBIAS 1215..1263
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 509..551
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000255"
FT BINDING 517
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 550
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 558
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 572..573
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 1147
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT BINDING 1156..1157
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000250"
FT CONFLICT 248
FT /note="S -> P (in Ref. 2; BAA87224)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1273 AA; 142490 MW; 3FEFF6433DF3C0B6 CRC64;
MPLGRSSWIC CAKYFVNTKS RFNEILPPRF TLIVSFYSMN TSENDPDGHY DFPEMTEHHS
DRASSYANAN NVNSTQPQLV SSEQALLAIL GGGLQSITPN SVNQNAYSRS TYRTDGGLNS
QPVSSLNNQW GNYNPAFLPS RYDSSFHPYT ISQAANQPFP QHLLGNSNAG VAQQSGMRTI
GLPPTVGSSF PQQKSSTYEN FFDANSPSSQ QFPSTYPSRS QNPLSSSGDG STAIHAGPIQ
HQNSNAFSNY PYPLDASHLS SQQLLSMYRD QVSHGVTPST FRNHESFMPT QLVSATELSK
SVDNAVLPIP PTTAPAVVSP PASSFPLMSS AATSGNISSP ALFDSELGAR PEGSVAIEPS
RVLLQWSSQS SSHTIPSAGA SIPTSSLKSF FEHAAEAARK CNLDPRALES FEQHMLSDRL
HDPVVLFHYF QIRNSICWLW IKNPTHAISR VEAQGVCVDR CLFQLASLAY EFLVRYGYIN
YGCLSFDSSF TNETNTGTTS SSASKQKTIA VVGAGLTGLI CARQLTGLFS QYSSSFLSKN
ELPPKVIILE AKERTGGRIY SRALPVSHTS ATQINHHTSN SNSISSNSTS LNPKDVTDPS
HIPSAIDLGF QFLFSPMDDI LLNLLNKQLG IEVTEMTGSD LVYDETDTKV LDMVEVKKLN
ILWEKLLEYV SVCFFINVEE SVRISWISQF QLFIDEMFPD HLSKSLSLNA SHEFSFKKTM
LILIDEVSSY AKLGNSQKKF LIWCFKVAEL DDTLYPLNTV DTDFSKDILI PKVARRGLSQ
LPWALQSYPS PLNIHYEKFV SKVTIENDKC TLDCKDNSSY EVDQVVIACS PSHFSSNIEF
SPGLPNFVTE NIKSIDFKPG KKVILRYAAA FWRKNIRSFG IIPKSLSQEM NNDENDGKSC
FVLRIWNMLP ETGVPILVAD INPQMTSSSS NETSHLIQEL HSLIVDHFQN DSNSSADLLD
AWVTNWSRNG VYDGLNSYPN FANDKQQYEK RFRQSQLSYN LGRLHIAGDY IFSCVGCRTL
QRSFLSGLSV CTGIIDSLAP ISLTIPIIGE TSRKELDQFL RNSKVNNFDP NAEAQRHLSY
QARYRLKKQE RLDEHKEEQE QLVTELLGYL PEPPSKPNAN PFLLYQKMQW HVCRALADED
KRRLTGDSTA KATINETRAK LGKTWRQLDD LGKKPWIDEI AAQREAYAGK ILRYQRLTKE
YEMRAEQIRN DYAAKCQDEP IPDDEARLFM QAQREEEQRK QTQDDNISKS REASDEEYHD
DGSSDSGYNG TRY
